3AO2

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L3UPDB ENTRY 3L3U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62931.8M AmSO4, 0.15M Na CITRATE pH 4.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.16α = 90
b = 49.16β = 90
c = 103.12γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2008-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.957Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.85099.40.0370.04127.75.62583725677
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.9150.160.189.75.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3L3U1.826.75258372441712851000.188520.187020.2173RANDOM25.29
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.020.010.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.484
r_dihedral_angle_3_deg15.1
r_dihedral_angle_4_deg8.066
r_dihedral_angle_1_deg5.698
r_scangle_it3.832
r_scbond_it2.543
r_mcangle_it1.962
r_angle_refined_deg1.688
r_mcbond_it1.186
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.484
r_dihedral_angle_3_deg15.1
r_dihedral_angle_4_deg8.066
r_dihedral_angle_1_deg5.698
r_scangle_it3.832
r_scbond_it2.543
r_mcangle_it1.962
r_angle_refined_deg1.688
r_mcbond_it1.186
r_nbtor_refined0.299
r_symmetry_vdw_refined0.247
r_nbd_refined0.2
r_xyhbond_nbd_refined0.175
r_metal_ion_refined0.164
r_symmetry_hbond_refined0.124
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2092
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms77

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling